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Shape Screening

Efficient ligand-based virtual screening of millions to billions of molecules

Screen ultra-large libraries quickly


Shape Screening is a ligand-based workflow for efficiently screening ultra-large purchasable or synthesizable compound libraries. Chemically-intuitive ligand alignments are scored based on the quality of the shape overlap against a reference ligand. Shape Screening identifies potential hit molecules with activity even when they are topologically dissimilar to the known reference ligand, making it a powerful ligand-based screening method.

Access multiple Shape Screening workflows from a single access license

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Quick Shape

Store and screen tens to hundreds of billions of molecules at speeds exceeding Shape GPU performance by 30% as well as reducing hard disk requirements by a factor of 100

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Shape GPU

Perform GPU-accelerated high-throughput virtual screenings on millions of molecules with ~11,000 comparisons per second

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Shape CPU

Screen hundreds of thousands to millions of molecules quickly on multiple CPUs

Key Capabilities

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Generate intuitive and information rich, high-quality 3D alignments of common scaffolds
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Identify true hits in libraries from one to over one billion compounds
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Jump-start your screening with prepared compound libraries from vendors including Enamine, Mcule, Molport, WuXi, Millipore Sigma, and Sigma-Aldrich
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Access multiple Shape Screening workflows from a single access license

Description of Shape Screening Workflows

Workflow Description Library Size Time to screen 4.0B (days) Time to screen 6.5B (days) Storage space for 6.5B (TB)
Quick Shape Combination of 1D-SIM* prefilter and Shape CPU Screening > 4.0 billion 5.2 5.5‡ 0.4
Shape GPU GPU-accelerated 3D screening < 5.0 billion 4.6 7.5‡ 33
Shape CPU CPU-based 3D screening < 10 million NA NA NA

QuickShape screening in the age of ultra-large libraries

Learn about QuickShape, an automated staged workflow combining both 1D and 3D approaches, which enables efficient 3D-Shape screenings for library sizes in the tens of billions of molecules.

Save compute time and effort using prepared commercial libraries for Shape Screening

Schrödinger has partnered with leading providers to help you access commercial databases of fragments, lead-like, near drug-like, and drug-like compounds ranging from millions to billions of compounds encompassing a vast chemical space.

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Prepared Commercial Libraries

Fully prepared databases of purchasable compounds


Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

Life Science
Shape-Based Virtual Screening of a Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors
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Structure-based virtual screening of MT2 melatonin receptor: Influence of template choice and structural refinement
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Exploring Conformational Search Protocols for Ligand-based Virtual Screening and 3-D QSAR Modeling
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Boosting virtual screening enrichments with data fusion: Coalescing hits from two-dimensional fingerprints, shape, and docking

Training & Resources

Online certification courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.


Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.